We describe a new species of murine rodent from a skull collected on Bisa Island and 3 specimens from Obi Island, North Maluku Province, Indonesia. Molecular and morphological data indicate a close relationship with Halmaheramys bokimekot (Fabre et al. 2013). The new species is characterized by its combination of large size; short tail with large scales; spiny, coarse, dark dorsal pelage with long black guard hairs; and a dark gray ventral pelage that contrasts slightly with the dorsum. The Bisa specimen displays unusual zygomatic arch morphology, which may be a disease-related deformity, or potentially a sexually dimorphic trait. The new species shares several external and cranio-mandibular features with its sister species from Halmahera that differ from those of Rattus species, including a spiny pelt, deep palatine sulci, a high rostrum and relatively flat dorsal profile, short incisive foramina, short palatal bridge, and molars with simple occlusal patterns. Although certain morphological characteristics of the new taxon suggest an affinity with the taxonomically diverse and geographically widespread Rattus, in other respects it clearly fits into the Wallacean clade containing Bunomys, Paruromys, and Taeromys, as indicated by molecular phylogenetic analyses. Along with the recent discovery of Halmaheramys, recognition of this new species from Bisa and Obi Islands underscores the north Moluccan region's high endemism, conservation importance, and the urgent need for a better inventory of its biodiversity.